Synthesis and anti-proliferative effect of benzimidazole derivatives

ABSTRACT

This invention provides for compounds, compositions, and methods that involve anti-proliferative and anti-neoplastic activity in cancer cells. In particular, a series of benzimidazole, purine, imidazopyridine, and imidazopyrizine compounds having selected substitution patterns are disclosed, and the activity of various subject compounds is demonstrated. For example, the invention provides compounds having the general formula: 
                         
their pharmaceutical compositions, and methods of treatment using the subject compounds and compositions.

This application claims the benefit of U.S. Provisional Application No.61/025,462, filed Feb. 1, 2008, the disclosure of which is incorporatedherein by reference in its entirety.

GOVERNMENT LICENSE RIGHTS

The U.S. Government has a paid-up license in this invention and theright in limited circumstances to require the patent owner to licenseothers on reasonable terms as provided for by the terms of Grant No.5P20MD000215-070002 awarded by the National Institutes of Health,National Center on Minority Health and Health Disparities, to SpelmanCollege.

FIELD OF THE INVENTION

The invention is related to compounds, compositions, and methods thatinvolve anti-proliferative and anti-neoplastic activity in cancer cells.

BACKGROUND OF THE INVENTION

It is estimated that 10.1 million Americans have a medical history thatinvolves cancer, and it is expected that another 1.4 million new caseswill develop in the next year. Cancer is the second leading cause ofdeath among Americans, with prostate cancer being the leading form foundin men. Unfortunately, the statistics surrounding the disease arecomplicated by disparities relating to race and sex and by decliningrelative survival rates. For general information, see: American CancerSociety, Cancer Facts and Figures 2008, Atlanta: American CancerSociety, 2008.

Prostate cancer, which is being increasingly diagnosed in younger-agedmen, often metastasizes to other places in the body and therefore isdifficult to regulate. Studies have shown that the cellular survivalpathways present in the cancerous tissues of the prostate, and where itspreads in the body, are resistant to the normal apoptosis processesthat constitute a principal type of programmed cell death (PCD) in acomplex organism. Thus, cancerous cells are able to avoid apoptosis andreplicate in an unregulated manner, causing malignant tumors to form.Some causes for the rapid cell growth in the prostates of men are due toage and the presence of mutated genes that encode proteins for celldivision. See: Kleinsmith, L. J., Principles of Cancer Biology, PearsonBenjamin Cummings (2006). Further, studies of the genetic make up ofAfrican American males diagnosed with prostate cancer have associated anover-expression of the gene Bcl-2 that prevents apoptosis with thecancer. Moreover, Bcl-2 has also been linked to other fatal cancers likebreast cancer and leukemia in children.

Celecoxib, an FDA-approved drug, is known to induce apoptosis byinhibiting the PDK1/Akt interaction in a process independent of itscyclooxygenase-2 (COX-2) activity. Its PDK1 activity has been directlylinked to its ability to inhibit cell growth in prostate cancer cells.Exploiting the activity of celecoxib, Zhu et al. developed a library ofmolecules which included the efficacious compound known as OSU-03013.This celecoxib derivative diminished cell proliferation by inhibitingPDK1 in PC-3 cells in micromolar concentrations thirty-fold lower thanthat of celecoxib. The versatility of OSU-03013 in treating a number oftumors, and its ability in overcoming the chemotherapeutic resistance ofsome drugs have been noted.

While the activity of these compounds has been attributed to theirbinding to the catalytic domain of PDK1 and the subsequent inhibition ofAkt activation, the mechanism of action has not been fully identified.Further, the ability of celecoxib to inhibit cell proliferation has beenattributed to mechanisms associated with the reduction of inflammationsand the inhibition of the COX-2 enzyme. See: Cui, W. et al., Anti-CancerDrugs (2008), 19(9), 891-897; Szabo, I. et al., J. Phys. (Paris), 2001,95, 379-383; Yoshinaka, R. et al., Anticancer Research (2006), 26(6B),4245-4254; and Mukherjee, P. et al., J. of Immunology (2008), VolumeDate 2009, 182(1), 216-224. In comparison to other, more potent COX-2inhibitors, celecoxib displayed a superior potency in inducing apoptosisin comparison to other COX-2 inhibitors. See: Kazanov, D. et al., Clin.Cancer Res., 2004, 10, 267-271; and Srinath, P. et al., Anticancer Res.,2003, 23, 3923-3928. The compound's ability to induce apoptosis byvarious routes adds to its appeal as a chemotherapeutic agent and a leadmolecule. Analogs of celecoxib could potentially be active againstmalignant growth and be useful as a Non-steroidal Anti-inflammatory Drug(NSAID) with enhanced oral activity and superior safety to that ofcelecoxib. Such a molecule would vastly improve the treatments forcancer and inflammation based diseases.

Thus, new compounds are needed that might function in a fashion similarto celecoxib and possibly help identify the structural and electronicfeatures of a molecule that give rise to such activity. In addition, newcompounds are needed that might exhibit anti-proliferative oranti-neoplastic activity, regardless of the specific mechanism by whichsuch activity might arise. Therapeutically effective agents,particularly those that are effective in humans and other mammals, areneeded to treat such diseases, to increase the survivability of thepatient, inhibit the rapidly-proliferating cell growth associated withthe neoplasm, and/or effect a regression of the neoplasm.

BRIEF SUMMARY OF THE INVENTION

In one aspect, the present invention provides a series of compounds thatexhibit anti-proliferative activity, including activity against humanprostate cancer cells. Therefore, methods for treating and/or preventinga neoplasia are provided herein. The compounds disclosed herein includesubstituted benzimidazole, purines, imidazopyridine, and imidazopyridinespecies, which are shown to inhibit cell proliferation in PC-3 cells.This invention also provides methods of making the inventive compounds,and methods of treating and/or preventing cancer using the inventivecompounds.

As used herein, the term “treatment” is non-limiting and includes thepartial or total inhibition of the neoplasia growth, spreading, ormetastasis, or partial or total destruction of the neoplasia cells. Theterm “prevention,” as used herein, is also non-limiting, and includeseither preventing the onset of clinically evident neoplasia altogether,or preventing the onset of a preclinically evident stage of neoplasia inindividuals at risk. The prevention of initiation for malignant cells orarresting or reversing the progression of premalignant cells tomalignant cells are also intended to be encompassed by this definition.Therefore, prevention includes the prophylactic treatment of those atrisk of developing the neoplasia. Also as used herein, the phrase“therapeutically-effective,” as in describing atherapeutically-effective amount of a drug or dosage form, is intendedto qualify an amount of an agent that will achieve the goal ofimprovement in disease severity or the frequency of incidence.Typically, the phrase therapeutically-effective involves theminimization or, if possible, the avoidance of adverse side effectsassociated with many therapies. The term “neoplasia” is intended to benon-limiting, and includes any abnormal new growth, or tumor, which maybe benign or malignant. Thus, neoplasia includes, but is not limited to,neoplasia that produce prostaglandins or express a cyclooxygenase,including benign and cancerous tumors, growths, and polyps.

In one aspect, this invention provides a compound having the formula:

wherein

is selected from:

wherein G is selected from

wherein Z is selected from CH₂, NH, O, or S;

wherein Q is selected from CH₂, NH, O, or S;

wherein n is 0, 1, 2, or 3; or

wherein X in each occurrence is selected from hydrogen; a halide (F, Cl,Br, or I); a linear or branched alkyl having up to 10 carbon atoms,optionally substituted with at least one halide; or an alkoxide having alinear or branched alkyl group having up to 10 carbon atoms, optionallysubstituted with at least one halide;wherein X^(D) is selected from

and Y is selected from O, or NH.

In one aspect, this invention provides a compound based on (I) havingthe formula:

wherein Y is selected from O or NH; and X is selected from hydrogen; ahalide (F, Cl, Br, or I); a linear or branched alkyl having up to 10carbon atoms, optionally substituted with at least one halide; or analkoxide having a linear or branched alkyl group having up to 10 carbonatoms, optionally substituted with at least one halide. For instance, Xcan be X^(A), wherein X^(A) is selected from H, CH₃, C(CH₃)₃, CF₃, OCF₃,C₆H₅, OCH₃, OC(CH₃)₃, or Cl.

An additional aspect of the invention provides a compound based on (I)having the formula:

wherein Ar can be selected from:

wherein X^(B) can be CH₃, C(CH₃)₃, or OCH₃;

wherein Z can be CH₂, NH, O, or S;

wherein Q can be CH₂, NH, O, or S; or

wherein n can be 0, 1, 2, or 3; and Y can be selected from O or NH.

Additionally, the invention provides a compound based on (I) having theformula:

or

whereinR can be

or

wherein X^(C) can be H, CH₃, or C(CH₃)₃; and Y can be selected from O orNH.

In yet another aspect, this invention also provides a compound based on(I) having the formula:

wherein X is selected from hydrogen; a halide (F, Cl, Br, or I); alinear or branched alkyl having up to 10 carbon atoms, optionallysubstituted with at least one halide; or an alkoxide having a linear orbranched alkyl group having up to 10 carbon atoms, optionallysubstituted with at least one halide;X^(D) can be

and wherein Y can be selected from O or NH. For instance, X can beX^(A), wherein X^(A) is selected from H, CH₃, C(CH₃)₃, CF₃, OCF₃, C₆H₅,OCH₃, OC(CH₃)₃, or Cl.

In yet another aspect, this invention also provides a compound based on(I) having the formula:

wherein Ar can be selected from

wherein X^(B) can be CH₃, C(CH₃)₃, or OCH₃;

wherein Z can be CH₂, NH, O, or S;

wherein Q can be CH₂, NH, O, or S;or

wherein n can be 0, 1, 2, or 3;X^(D) can be

and wherein Y can be selected from O or NH.

In another aspect, this invention provides a compound of the formula:

wherein J is selected from

wherein Z is selected from CH₂, NH, O, or S;

wherein Q is selected from CH₂, NH, O, or S;

wherein n is 0, 1, 2, or 3; or

wherein X in each occurrence is selected from hydrogen; a halide (F, Cl,Br, or I); a linear or branched alkyl having up to 10 carbon atoms,optionally substituted with at least one halide; or an alkoxide having alinear or branched alkyl group having up to 10 carbon atoms, optionallysubstituted with at least one halide;wherein X^(D) is selected from

and Y is selected from O or NH.

Further, this invention also provides a compound based on (II) havingthe formula:

wherein X is selected from hydrogen; a halide (F, Cl, Br, or I); alinear or branched alkyl having up to 10 carbon atoms, optionallysubstituted with at least one halide; or an alkoxide having a linear orbranched alkyl group having up to 10 carbon atoms, optionallysubstituted with at least one halide; and wherein Y can be selected fromO or NH. For instance, X can be X^(A), wherein X^(A) is selected from H,CH₃, C(CH₃)₃, CF₃, OCF₃, C₆H₅, OCH₃, OC(CH₃)₃, or Cl.

A further aspect of this invention provides for a compound based on (II)having the formula:

wherein Ar can be selected from

wherein X^(B) can be CH₃, C(CH₃)₃, or OCH₃;

wherein Z can be CH₂, NH, O, or S;

wherein Q can be CH₂, NH, O, or S; or

wherein n can be 0, 1, 2, or 3; and Y can be selected from O or NH.

Yet another aspect of this invention provides for a pharmaceuticalcomposition comprising a therapeutically-effective amount of at leastone compound according to the present disclosure, or apharmaceutically-acceptable salt thereof, and apharmaceutically-acceptable carrier. This composition may also compriseother pharmaceutically-acceptable excipients, stabilizers, diluents,adjuvants, preservatives, binders, coatings, disintegrants, sorbants, orother suitable additives or components as understood by one of ordinaryskill in the art.

Still another aspect of this invention provides for a method of treatinga neoplasia of any type in a mammalian subject, the method comprisingtreating the subject with a therapeutically-effective amount of at leastone compound according to the present disclosure, or apharmaceutically-acceptable salt thereof. This method includes treatingthe subject with a therapeutically-effective amount of a compositioncomprising the compound, as disclosed herein.

In another aspect, the present invention provides a method of making acompound according to any of formulas 1 through 27, as illustratedherein. The method of this disclosure can include the synthesis,purification, and/or isolation of the desirable compound.

These and other aspects of the present invention are provided in moredetail.

BRIEF DESCRIPTION OF THE FIGURE

FIG. 1 illustrates the dose dependent antiproliferative effects ofbenzimidazole compounds 206-208 (Table 1) using PC-3 human prostatecancer cells, using the DNA assay described in Example 9.

DETAILED DESCRIPTION OF THE INVENTION

The present invention affords compounds, compositions, and methods thatare useful for treating and/or preventing cancer. In particular, certainbenzimidazole molecules have been found to act as anti-proliferationagents. The subject benzimidazole compounds (1-9 and 22-27) typicallyare 2-substituted, with additional aryl, heteroaryl, and/or cycloalkylsubstitutions at the 1- or 7-positions. Similarly, the subjectimidazopyridine (10-13 and 16-19), imidazopyrazine (14 and 20), andpurine (15 and 21) compounds are 2-substituted, with additional aryl,alkyl, heteroaryl, and/or cycloalkyl substitutions at the 1 positions.The synthesis of the molecules was accomplished using Microwave AssistedOrganic Synthesis (MAOS), in which the desired molecules were obtainedin modest yields.

Cancers that can be treated and/or prevented using the compoundsdisclosed herein include, but are not limited to, brain cancer, bonecancer, epithelial cell-derived neoplasia (epithelial carcinoma) such asbasal cell carcinoma, adenocarcinoma, gastrointestinal cancer such aslip cancer, mouth cancer, esophageal cancer, small bowel cancer, stomachcancer, colon cancer, liver cancer, bladder cancer, pancreatic cancer,ovary cancer, cervical cancer, lung cancer, breast cancer, skin cancersuch as squamus cell and basal cell cancers, prostate cancer, renal cellcarcinoma, other known cancers that effect epithelial cells throughoutthe body, and fibrosis which can occur with radiation therapy. Inanother aspect, the compounds and methods disclosed herein can be usedto treat subjects having adenomatous polyps, including those withfamilial adenomatous polyposis (FAP), and additionally, can be used toprevent polyps from forming in patients at risk of FAP.

In addition to the treatment of cancer, the compounds disclosed hereincan be used in preparing a pharmaceutical composition for the treatmentand/or prevention of inflammatory diseases. Inflammatory diseases thatcan be treated and/or prevented using the compounds disclosed hereininclude but are not limited to the group consisting of infectiousdisease; psoriasis; psoriatic arthritis; rheumatoid arthritis;osteoarthritis; juvenile chronic arthritis; inflammatory bowel disease(IBD); irritable bowel syndrome (IBS); ulcerative colitis; Crohn'sdisease; diverticulosis; pancreatitis, type I diabetes (IDDM); GravesDisease; an immune-mediated renal disease; infectious, autoimmunechronic active hepatitis; primary biliary cirrhosis; granulomatoushepatitis; sclerosing cholangitis; multiple sclerosis (MS); idiopathicdemyelinating polyneuropathy; Guillain-Barre syndrome; chronicinflammatory demyelinating polyneuropathy, systemic lupus erythematosus(SLE); amyloidosis; myasthenia gravis; splenomegaly; transplantrejection; graft-versus-host disease; atherosclerosis;spondyloarthropathies; systemic sclerosis; idiopathic inflammatorymyopathies; Sjogren's syndrome; systemic vasculitis; sarcoidosis;autoimmune hemolytic anemia; autoimmune thrombocytopenia; thyroiditis;gluten-sensitive enteropathy; endotoxemia; septicemia; toxic shocksyndrome; a bullous skin disease; erythema multiform; atopic dermatitis;psoriasis; contact dermatitis; neutrophilic dermatoses; cystic fibrosis;allergic asthma; allergic rhinitis; food hypersensitivity; urticaria;eosinophilic pneumonia; idiopathic, pulmonary fibrosis; adultrespiratory disease (ARD); acute respiratory distress syndrome (ARDS);asthma; chronic obstructive pulmonary disease (COPD); airwayhyper-responsiveness; chronic bronchitis; hypersensitivity pneumonitis;septic shock; transplant rejection and graft-versus-host disease (GVHD);and multiple organ failure.

For the compounds disclosed herein, more than one reaction scheme may beprovided for preparing a compound. The reaction schemes that are notspecifically provided for the preparation of a stated compound areapplicable for its synthesis, if the appropriate substitutions can beprovided for in the precursors, starting materials, or reagents employedin that scheme.

In one aspect, this invention provides a compound having the formula:

wherein

is selected from:

wherein G is selected from

wherein Z is selected from CH₂, NH, O, or S;

wherein Q is selected from CH₂, NH, O, or S;

wherein n is 0, 1, 2, or 3; or

wherein X in each occurrence is selected from hydrogen; a halide (F, Cl,Br, or I); a linear or branched alkyl having up to 10 carbon atoms,optionally substituted with at least one halide; or an alkoxide having alinear or branched alkyl group having up to 10 carbon atoms, optionallysubstituted with at least one halide;wherein X^(D) is selected from

and Y is selected from O or NH.

In one aspect, the present invention provides a compound based on (I)having the formula:

wherein Y can be selected from O or NH; and X is selected from hydrogen;a halide (F, Cl, Br, or I); a linear or branched alkyl having up to 10carbon atoms, optionally substituted with at least one halide; or analkoxide having a linear or branched alkyl group having up to 10 carbonatoms, optionally substituted with at least one halide. For instance, Xcan be X^(A), wherein X^(A) is selected from H, CH₃, C(CH₃)₃, CF₃, OCF₃,C₆H₅, OCH₃, OC(CH₃)₃, or Cl.

Compounds having the templates according to formulas 1 and 2 may beprepared at least as exemplified in Scheme 1 provided in Example 1.Scheme 1 also is applicable to many other related aryl substitutedbenzimidazole compounds, with the appropriate selection of substitutionin the precursors, starting materials, or reagents. While Scheme 1presents a specific synthetic method for a compound 1 template, thisscheme is also applicable to compounds having the formula 2, in whichthe benzoyl chloride is selected according to the desired template,Example 2. For example, compound 2 may be prepared according to Scheme 1using the substituted benzoyl chloride

The synthesis of compounds corresponding to formula 3 can beaccomplished at least as exemplified in Scheme 2 of Example 3.

An additional aspect of the invention provides compounds based on (I)having the formula:

Ar can be selected from:

wherein X^(B) can be CH₃, C(CH₃)₃, or OCH₃;

wherein Z can be CH₂, NH, O, or S;

wherein Q can be CH₂, NH, O, or S; or

wherein n can be 0, 1, 2, or 3; and Y can be selected from O or NH.Compounds corresponding to formula 4 and 5 can be prepared in a fashionanalogous to that exemplified in Scheme 1 when the appropriate aromaticamine derivative and substituted benzoyl chloride are used as inExamples 1 and 2. Compounds corresponding to formula 6 can be preparedin a fashion analogous to that exemplified in Scheme 2 when theappropriate aromatic amine derivative Example 3.

Additionally, the invention provides compounds based on (I) having theformula:

wherein R can be

wherein X^(C) can be H, CH₃, or C(CH₃)₃; and Y can be selected from O orNH. Compounds corresponding to formulas 7 and 8 can be prepared in afashion at least as exemplified in Scheme 3 when the appropriatealiphatic amine derivative and substituted benzoyl chloride are used.The aliphatic amines will be substituted for compound 119 and can beselected from

wherein X^(c) can be H, CH₃, or C(CH₃)₃, as appropriate. Compoundscorresponding to formula 9 can be prepared in a fashion at least asexemplified in Scheme 4 when the appropriate aliphatic amine derivativeand substituted benzoyl chloride are used.

Yet another aspect of this invention provides for additional compoundsbased on (I) having the formula:

wherein X is selected from hydrogen; a halide (F, Cl, Br, or I); alinear or branched alkyl having up to 10 carbon atoms, optionallysubstituted with at least one halide; or an alkoxide having a linear orbranched alkyl group having up to 10 carbon atoms, optionallysubstituted with at least one halide; and X^(D) can be

and wherein Y can be selected from O or NH. For instance, X can beX^(A), wherein X^(A) is selected from H, CH₃, C(CH₃)₃, CF₃, OCF₃, C₆H₅,OCH₃, OC(CH₃)₃, or Cl.

Scheme 5 can be applied towards the synthesis of compounds of formulas10-13 when X^(D) is

using the appropriate halogen substituted nitro pyridine

and substituted benzoyl chloride. Likewise, compounds of formulas 14 or15 when X^(D) is

can be synthesized according to Scheme 5 using the reagent

respectively and the appropriate substituted benzoyl chloride.

Scheme 6 can be applied for the preparation of compounds of the formulas10-13 having the disclosed X substituents and wherein X^(D) is

wherein Y can be NH or O, using the appropriate halogen substitutednitro pyridine. Likewise, compounds of the formulas 14 or 15 having thedisclosed X substituents and wherein X^(D) is

wherein Y can be NH or O, can be synthesized according to Scheme 6 usingthe reagents

respectively.

Further, this invention also provides a compound based on (I) having theformula:

wherein Ar can be selected from

wherein X^(B) can be CH₃, C(CH₃)₃, or OCH₃;

wherein Z can be CH₂, NH, O, or S;

wherein Q can be CH₂, NH, O, or S; or

wherein n can be 0, 1, 2, or 3; X^(D) can be selected from

and wherein Y can be selected from O or NH.

Scheme 5 can be applied towards the synthesis of molecules following theformula 16-19 when X^(D) is

using the appropriate substituted benzoyl chloride and one of thefollowing halogen substituted nitro pyridines:

Likewise, compounds following the formula 20 or 21 when X^(D) is

can be synthesized according to Scheme 5 using the reagents

respectively, and the appropriately substituted benzoyl chloride.

Scheme 6 can be applied for the preparation of compounds following theformula 16-19 having the disclosed X substituents and wherein X^(D) is

wherein Y can be NH or O, using the appropriate halogen substitutednitro pyridine. Likewise, compounds following the formula 20 or 21having the disclosed X substituents and wherein X^(D) is

wherein Y can be NH or O, can be synthesized according to Scheme 6 usingthe reagents

respectively.

In another aspect, this invention provides a compound of the formula:

wherein J is selected from

wherein Z is selected from CH₂, NH, O, or S;

wherein Q is selected from CH₂, NH, O, or S;

wherein n is 0, 1, 2, or 3; or

wherein X in each occurrence is selected from hydrogen; a halide (F, Cl,Br, or I); a linear or branched alkyl having up to 10 carbon atoms,optionally substituted with at least one halide; or an alkoxide having alinear or branched alkyl group having up to 10 carbon atoms, optionallysubstituted with at least one halide;wherein X^(D) is selected from

and Y is selected from O or NH.

A further aspect of this invention provides for a compound based on (II)having the formula:

wherein Y can be selected from O or NH; and X is selected from hydrogen;a halide (F, Cl, Br, or I); a linear or branched alkyl having up to 10carbon atoms, optionally substituted with at least one halide; or analkoxide having a linear or branched alkyl group having up to 10 carbonatoms, optionally substituted with at least one halide. For instance, Xcan be X^(A), wherein X^(A) is selected from H, CH₃, C(CH₃)₃, CF₃, OCF₃,C₆H₅, OCH₃, OC(CH₃)₃, or Cl. Compounds of formulas 22-23 may be preparedat least according to Scheme 7, provided in Example 14. The synthesis of22 is illustrated in Scheme 7 as shown. The synthesis of 23 may beachieved by using the reagent

in lieu of 113. Compounds of formula 24 may be prepared at leastaccording to Scheme 9 using the appropriate reagents based on thesubstituents as required in the final compound.

A further aspect of this invention provides for a compound based on (II)having the formula:

wherein Ar can be selected from

wherein X^(B) can be CH₃, C(CH₃)₃, or OCH₃;

wherein Z can be CH₂, NH, O, or S;

wherein Q can be CH₂, NH, O, or S; or

wherein n can be 0, 1, 2, or 3; and Y can be selected from O or NH.Compounds of formulas 25-26 may be prepared at least according to Scheme7 using the appropriate Grignard reagent and substituted benzoylchloride, provided in Example 14. Compounds of formula 27 may beprepared at least according to Scheme 9 using the appropriate Grignardreagent.

In a particular aspect of formula 1, wherein X is —CH₃, thebenzimidazole derivative is4-(1-p-tolyl-1H-benzo[d]imidazol-2-yl)benzenesulfonamide—a compoundhaving the chemical structure:

In yet another particular aspect of formula 1, wherein X is —C(CH₃)₃,the benzimidazole derivative is4-(1-(4-tert-butylphenyl)-1H-benzo[d]imidazol-2-yl)benzenesulfonamide—acompound having the chemical structure:

In a particular aspect of formula 4, wherein —Ar is

the benzimidazole derivative is4-(1-(naphthalen-2-yl)-1H-benzo[d]imidazol-2-yl)benzenesulfonamide—acompound having the chemical structure:

In another particular aspect of formula 4, wherein —Ar is

and Z is —CH₂—, the benzimidazole derivative is4-(1-(4-benzylphenyl)-1H-benzo[d]imidazol-2-yl)benzenesulfonamide, acompound having the chemical structure:

In yet another particular aspect of formula 4, wherein —Ar is

and Z is O, the benzimidazole derivative is4-(1-(4-phenoxyphenyl)-1H-benzo[d]imidazol-2-yl)benzenesulfonamide, acompound having the chemical structure:

In yet another particular aspect of formula 4, wherein —Ar is

the benzimidazole derivative is4-(1-(biphenyl-4-yl)-1H-benzo[d]imidazol-2-yl)benzenesulfonamide, acompound having the chemical formula:

The PDK1/Akt mechanism is a component in the development and progressionof prostate cancer. PDK1 is over-expressed in a number of tumor cellsand the inhibition of PDK1 kinase has been linked to the induction ofmitochondrial-mediated apoptosis and decreased proliferation in the PC-3human prostate cancer cell line. Therefore, due to its role in cancerand the regulation of cell cycle, PDK1 is an excellent target fordevelopment of chemotherapeutic agents for prostate cancer. While notintending to be bound by theory, one aspect of this invention includesthe evaluation of the three-dimensional steric and electronic featuresof the potential binding interactions of proposed or test molecules, forexample, when docked in the ATP binding pocket of PDK1. Again, while notbound by theory, useful pharmacophores that are disclosed herein mayhave some of the following properties: large hydrophobic substituents,which in various aspects may include aromatic or cycloaliphaticsubstituents; at least one hydrogen bonding substituent; aheteroaromatic central ring; and small hydrophobic substituents In oneaspect, for example, in characterizing the structure-activity ofcelecoxib analogs or derivatives, it was found that useful compoundscontained aromatic hydrophobic groups. Again, while not intending to bebound by theory, it is believed that a so-called “fuzzy” pharmacophore,which roughly describes very delocalized potential pi-pi (π-π)interactions involving the protein and an aromatic group, may be useful.For example, such an interaction in which a phenanthrene group of acelecoxib analog is docked in the aromatic rich ATP binding pocket ofPDK1 appears to afford stable conformations.

In a further aspect, useful pharmacophores of this invention that havethe ability to inhibit PDK1 kinase activity and proliferation in PC-3cells can have particular relationships between their electronic andsize and/or shape features their. In this aspect, for example, usefulpharmacophores can have size to lipophilicity ratios, calculated by theratio of molar volume (in cm³/mol) to lipophilicity (as c Log P) ratiosin the range from about 50 to about 90. In another aspect, usefulpharmacophores can have size to lipophilicity ratios in the range fromabout 60 to about 85, or from about 65 to about 80. For example,compounds 206-208 of Table 1 have ratios of molar volume (in cm³/mol) tolipophilicity (as c Log P) of 78, 69, and 67, respectively.

TABLE 1 Activity of Benzimidazole Compounds and Comparative Moleculesfor the Inhibition of PC-3 Cells. MOLAR PC3 VOLUME No. COMPOUND IC₅₀(μM) (cm³/mol) cLogP 201

30 284 3.41 202

3 333 5.17 203

32 312 5.31 204

18 309 4.7 205

10 298 4.14 206

24 287 3.66 207

20 350 5.08 208

10 301 4.49

In addition to evaluating the activity of the inventive benzimidazole,purine, imidazopyridine, and imidazopyrizine compounds for theinhibition of PC-3 cells, a number of other methods for biologicaltesting may be used for the inventive compounds. For example, othermodels and tests that can be used include, but are not limited to, theMurine Lewis lung Carcinoma Model, Human prostate cancer cell tumors,LNCaP, and the following cell lines and growth studies.

Cell lines that can be used include, but are not limited to, classicsmall cell lung cancer (SCLC) cell lines NCI-H209, NCI-H345, andNCI-H510; variant SCLC cell lines NCI-N417 and NCI-H82; large cellcarcinoma cell line NCI-H1155; adeno carcinoma cell line NCI-H23; andbronchioalveolar carcinoma cell line A549, breast cancer cell line MCF-7(American Type Tissue Culture Rockville Md.; ATCC) and colon cancer celllines such as NCI-H630 (ATCC), HT 29, SW948, HCA-7; prostate cancer celllines PC3, LNCap, MDA Pca 2a, MDA Pca 2b; and others that can be testedin vivo or in vitro. Growth studies that can be used include, but arenot limited to, a modification (Promega CellTiter 96®, Promega Madison,Wis.) of the semiautomated colorimetric assay, MTT (Nakanishi, et al.Exper. Cell Biol. 1988, 56, 74-85), which quantifies cell numbers basedon reduction of a tetrazolium compound by tumor cells as determined by aspectrophotometer (540 nm) is used. Other tumor models that can be usedare disclosed in U.S. Pat. No. 6,469,040 and those defined theDevelopmental Therapeutics Program NCI/NIH (dtp.nci.nih.gov/index.html),the entirety of which is incorporated herein by reference in itsentirety.

Other potential cell lines include, but are not limited to, thefollowing: Leukemia cell lines P388, P388/ADR, CCRF-CEM, HL-60(TB),K-562, MOLT-4, RPMI-8226, and SR; non-small cell lung cell lines LXFL529, A549/ATCC, EKVX, HOP-62, HOP-92, NCI-H226, NCI-H23, NCI-H322M,NCI-H460, and NCI-H522; colon cell lines DLD-1, KM20L2, COLO 205,HCC-2998, HCT-116, HCT-15, HT29, KM12, and SW-620; CNS cell linesSNB-78, XF 498, SF-268, SF-295, SF-539, SNB-19, SNB-75, and U251;melanoma cell lines RPMI-7951, M19-MEL, LOX IMVI, MALME-3M, M14,MDA-MB-435, SK-MEL-2, SK-MEL-28, SK-MEL-5, UACC-257, and UACC-62;ovarian cell lines IGR-OV1, OVCAR-3, OVCAR-4, OVCAR-5, OVCAR-8,NCI/ADR-RES, and SK-OV-3; renal cell lines RXF-631, SN12K1, 786-0, A498,ACHN, CAKI-1, RXF 393, SN12C, TK-10, and UO-31; prostate cancer celllines PC-3 and DU-145; breast cancer cell lines MDA-MB-468, MCF7,MDA-MB-231/ATCC, HS 578T, MDA-N, BT-549, and T-47D; small cell lung celllines DMS 114 and SHP-77.

The benzimidazole, purine, imidazopyridine, and imidazopyrizinecompounds provided herein may be administered by any suitable routeknown to those skilled in the art, preferably in the form of apharmaceutical composition adapted to such a route, and in a doseeffective for the treatment intended. The active compounds andcomposition may, for example, be administered orally, intravascularly,intraperitoneally, intranasal, intrabronchial, subcutaneously,intramuscularly or topically (including aerosol). The administration ofthe present invention may be for either prevention or treatmentpurposes. The methods and compositions used herein may be used alone orin conjunction with additional therapies known to those skilled in theart in the prevention or treatment of neoplasia. Alternatively, themethods and compositions described herein may be used as conjunctivetherapy. By way of example, the anti-neoplastic agents disclosed hereinmay be administered alone or in conjunction with other anti-neoplasticagents, cyclooxygenase-2 inhibitors, other growth inhibiting agents, orother drugs or nutrients.

As used herein, the phrase “conjunctive therapy” (or “combinationtherapy”), in defining the use of an anti-neoplastic agent disclosedherein and another pharmaceutical agent, is intended to encompassadministration of each agent in a sequential manner in a regimen thatwill provide beneficial effects of the drug combination, and is intendedas well to encompass co-administration of these agents in asubstantially simultaneous manner, such as in a single formulationhaving a fixed ratio of these active agents, or in multiple, separateformulations for each agent. In another aspect, the present inventionalso provides for a pharmaceutical composition comprising atherapeutically-effective amount of at least one compound according tothe present disclosure, or a pharmaceutically-acceptable salt thereof,in association with at least one pharmaceutically-acceptable carrier.This composition may also comprise other pharmaceutically-acceptableexcipients, stabilizers, diluents, adjuvants, preservatives, binders,coatings, disintegrants, sorbants, or other suitable additives orcomponents as understood by one of ordinary skill in the art.

For oral administration, the pharmaceutical composition may be in theform of, for example, a tablet, a capsule, a suspension, a powder, aliquid, or a solution or any other suitable form. The pharmaceuticalcomposition can be made in the form of a dosage unit containing aparticular amount of the active ingredient(s). Examples of such dosageunits are capsules, tablets, powders, granules, or suspensions, withconventional additives such as lactose, mannitol, corn or potato starch,and the like; with binders such as crystalline or microcrystallinecellulose, cellulose derivatives, acacia, corn starch, or gelatins; withdisintegrators such as corn starch, potato starch, or sodiumcarboxymethyl-cellulose; and with lubricants such as talc or magnesiumstearate. The active ingredient may also be administered by injection asa composition wherein, for example, saline, dextrose or water may beused as a suitable carrier.

For intravenous, intramuscular, subcutaneous, or intraperitonealadministration, a compound of this invention may be combined with asterile aqueous solution that can be isotonic with the blood of therecipient. Such formulations may be prepared, for example, by dissolvingor suspending a solid active ingredient, which can be a neutral compoundor a salt, in water containing physiologically compatible substancessuch as sodium chloride, glycine, and the like. Such a solution orsuspension could have a buffered pH compatible with physiologicalconditions to produce an aqueous solution or suspension that could berendered sterile. The formulations may be present in unit or multi-dosecontainers such as sealed ampoules or vials.

If the neoplasia is localized in the G.I. tract, the compound may beformulated with acid-stable, base-labile coatings known to one of skillin the art which begin to dissolve in the high pH small intestine.Formulations to enhance local pharmacologic effects and reduce systemicuptake are typical.

Formulations suitable for parenteral administration typically cancomprise a sterile aqueous preparation of the active compound which isusually made isotonic. Preparations for injections may also beformulated by suspending or emulsifying the compounds in non-aqueoussolvent, such as vegetable oil, synthetic aliphatic acid glycerides,esters of higher aliphatic acids, propylene glycol, or other suitablesubstances.

Formulations for topical use include gels, creams, oils, and the like,known to one of ordinary skill in the art. For example, aerosol deliverycompositions could be prepared by formulating the compounds with knownaerosol excipients, such as saline, and administered the formulationusing commercially available nebulizers. Formulation in a fatty acidsource may be used to enhance biocompatibility. For example, aerosoldelivery is a typical method of delivery for epithelial neoplasias ofthe lung for prevention application.

For rectal administration, the active ingredient may be formulated intosuppositories using bases which are solid at room temperature and meltor dissolve at body temperature. For example, commonly used basesinclude cocoa butter, glycerinated gelatin, hydrogenated vegetable oil,polyethylene glycols of various molecular weights, and fatty esters ofpolyethylene stearate.

The dosage form and amount can be readily established by reference toknown neoplasia treatments or prophylactic regiments. For example, theamount of therapeutically active compound that is administered and thedosage regimen for treating a disease condition with the compoundsand/or compositions of this invention depends on a variety of factors,including the age, weight, sex and medical condition of the subject, theseverity of the disease, the route and frequency of administration, andthe particular compound employed. The amount and dosage regimen oftherapeutically active compound also can depend on the location of theneoplasia, as well as the pharmacokinetic properties of the individualtreated, and thus may vary widely. Such dosage generally will be lowerif the compounds are administered locally rather than systemically, andfor prevention rather than for treatment. Such treatments may beadministered as often as necessary and for the period of time judgednecessary by the treating physician.

One of skill in the art will appreciate that the dosage regime ortherapeutically effective amount of the inhibitor to be administratedmay need to be optimized for each individual. The pharmaceuticalcompositions may contain active ingredient in the range of, for example,from about 0.1 to about 2000 mg, or in the range from about 0.5 to about500 mg, or from about 1 to about 200 mg, though these amounts are notconsidered limiting. A daily dose from about 0.01 to about 100 mg/kgbody weight is typical, which also can be from about 0.1 to about 50mg/kg body weight, or from about 1 to about 30 mg/kg, which may beappropriate. The daily dose can be administered in one to four or moredoses per day.

Although any methods, devices, and materials similar or equivalent tothose described herein can be used in the practice or testing of theinvention, the typical methods, devices and materials are hereindescribed. All publications and patents mentioned in the disclosure ofthis invention are incorporated herein by reference in their entireties,for the purpose of describing and disclosing, for example, theconstructs and methodologies that are described in the publications,which might be used in connection with the presently describedinvention. The publications discussed above and throughout the text areprovided solely for their disclosure prior to the filing date of thepresent application. Nothing herein is to be construed as an admissionthat the inventors are not entitled to antedate such disclosure byvirtue of prior invention. Moreover, it is also to be understood thatthe terminology used herein is for the purpose of describing particularaspects or embodiments and is not intended to be limiting. Should theusage or terminology used in any reference that is incorporated byreference conflict with the usage or terminology used in thisdisclosure, the usage and terminology of this disclosure controls.

For any particular compound disclosed herein, any general structurepresented also encompasses all conformational isomers, regioisomers, andstereoisomers that may arise from a particular set of substituents.Thus, the general structure also encompasses all enantiomers,diastereomers, and other optical isomers whether in enantiomeric orracemic forms, as well as mixtures of stereoisomers, as the contextrequires.

Also unless indicated otherwise, when a range of any type is disclosedor claimed, for example a range of molecular weights, molar volumes, cLog P, concentrations, temperatures, and the like, it is intended todisclose or claim individually each possible number that such a rangecould reasonably encompass, including any sub-ranges encompassedtherein. For example, when the Applicants disclose or claim a chemicalmoiety having a certain number of atoms, for example carbon atoms,Applicants' intent is to disclose or claim individually every possiblenumber that such a range could encompass, consistent with the disclosureherein. Thus, by the disclosure that an alkyl substituent or group canhave from 1 to 10 carbon atoms or “up to” 10 carbon atoms, Applicantsintent is to recite that the alkyl group have 1, 2, 3, 4, 5, 6, 7, 8, 9,or 10 carbon atoms, including any ranges, sub-ranges, or combinationsthereof between any number of carbon atoms recited herein. In anotherexample, by the disclosure that the ratio of molar volume (in cm³/mol)to lipophilicity (as c Log P) is in the range from about 65 to about 80,Applicants intent is to recite individually that the ratio can be about65, about 66, about 67, about 68, about 69, about 70, about 71, about72, about 73, about 74, or about 75, including any ranges, sub-ranges,or combinations thereof, between any of these ratios. Accordingly,Applicants reserve the right to proviso out or exclude any individualmembers of such a group, including any sub-ranges or combinations ofsub-ranges within the group, that can be claimed according to a range orin any similar manner, if for any reason Applicants choose to claim lessthan the full measure of the disclosure, for example, to account for areference that Applicants are unaware of at the time of the filing ofthe application.

All publications and patents mentioned in this disclosure areincorporated herein by reference in their entireties, for the purpose ofdescribing and disclosing, for example, the constructs and methodologiesthat are described in the publications, which might be used inconnection with the presently described methods, compositions, articles,and processes. The publications discussed throughout the text areprovided solely for their disclosure prior to the filing date of thepresent application. Nothing herein is to be construed as an admissionthat the inventors are not entitled to antedate such disclosure byvirtue of prior invention. Should the usage or terminology used in anyreference that is incorporated by reference conflict with the usage orterminology used in this disclosure, the usage and terminology of thisdisclosure controls. The Abstract of the disclosure is provided tosatisfy the requirements of 37 C.F.R. §1.72 and the purpose stated in 37C.F.R. §1.72(b) “to enable the United States Patent and Trademark Officeand the public generally to determine quickly from a cursory inspectionthe nature and gist of the technical disclosure.” The Abstract is notintended to be used to construe the scope of the appended claims or tolimit the scope of the subject matter disclosed herein. Moreover, anyheadings are not intended to be used to construe the scope of theappended claims or to limit the scope of the subject matter disclosedherein. Any use of the past tense to describe an example otherwiseindicated as constructive or prophetic is not intended to reflect thatthe constructive or prophetic example has actually been carried out.

The present invention is further illustrated by the following examples,which are not to be construed in any way as imposing limitations uponthe scope thereof. On the contrary, it is to be clearly understood thatresort may be had to various other aspects, embodiments, modifications,and equivalents thereof which, after reading the description herein, maysuggest themselves to one of ordinary skill in the art without departingfrom the spirit of the present invention or the scope of the appendedclaims. Thus, other aspects of this invention will be apparent to thoseskilled in the art from consideration of the specification and practiceof the invention disclosed herein.

In the following examples, unless otherwise specified, the syntheses andpreparations described therein were carried out under an inertatmosphere such as nitrogen or argon. Solvents were purchased fromcommercial sources and were typically dried prior to use. Unlessotherwise specified, reagents were obtained from commercial sources.

EXAMPLES Example 1 Synthesis of Aromatic-Substituted BenzimidazoleCompounds of Formula 1

The preparation of aromatic-substituted benzimidazole analogs wasaccomplished using the synthetic route outlined in Scheme 1. Undermicrowave irradiation, a 4-substituted aniline derivative 110 wascoupled to 1-fluoro-2-nitrobenzene 109 to give a nitro diaryl amine 111.Using a domestic microwave, the reaction produced yields greater than99.5% when the aniline substituent was an electron donating group. (See:Xu, Z.; Lu, Y.; Guo, Z-R. Synlett 2003, 564-566.) However, optimizingthe reaction conditions was difficult using a standard householdmicrowave and relied heavily on the placement of the vessel in themicrowave cavity to ensure reproducibility.

When the reaction was conducted in the CEM Discovery System, a singlemode industrial microwave able to maintain the temperature and pressureof the reaction mixture, the reaction time was decreased from 20 minutesto 5 minutes in some cases. The CEM reaction gave reproducible resultsand the crude reaction mixture showed no evidence of side products. Thenitro group of the diaryl amine was reduced using zinc and ammoniumchloride. After about 24 hours, approximately 90-100% of the nitrocompound 111 was reduced to the diamine 112. Ring formation was affordedfrom a condensation reaction of the diamine and the benzoyl chloride 113in two steps to give the target molecules of formula 1. For generalinformation, see: Goker, H., et al., Bioorganic. Medicinal Chemistry2002, 10, 2589-2596. The compounds corresponding to formula 4 wherein Aris 1-napthylenyl; 2-napthylenyl; phenanthrenyl; anthracenyl,

where n is 0, 1, 2, or 3; or other analogs disclosed herein can begenerated in a similar fashion as illustrated in Scheme 1, with theselection of an appropriate analog of compound 110 in the reactionscheme. The resulting compounds were or could be characterized by NMRspectroscopy, IR spectroscopy, melting point, and mass spectrometry.Among other ways, the benzoyl chloride 113 may be obtained by thereaction of the corresponding SO₂NH₂-substituted benzoic acid withSOCl₂, to obtain the desired benzoyl chloride 113.

Example 2 Synthesis of Aromatic-Substituted Benzimidazole Compounds ofFormula 2

Compounds of the formula

can be prepared according to Scheme 1, using the benzoyl chloride

for preparing the compounds. The substituents X, are defined herein. Thecompounds of formula 5 wherein Ar is 1-napthylenyl; 2-napthylenyl;phenanthrenyl; anthracenyl,

wherein n is 0, 1, 2, or 3; or other analogs disclosed herein can begenerated in a similar fashion as illustrated in Scheme 1, with theselection of an appropriate analog of compound 110 in the reactionscheme.

Hydantoin substituted benzoic acid can be treated with thionyl chlorideto prepare

Example 3 Synthesis of Aromatic-Substituted Benzimidazole Compounds ofFormula 3

The preparation of aromatic-substituted benzimidazole compounds offormula 3 was accomplished using the synthetic route outlined in Scheme2. Under microwave irradiation, a 4-substituted aniline derivative 110was coupled to 1-fluoro-2-nitrobenzene 109 to give a nitro diaryl amine111 as previously described. The diaryl amine 111 can be reduced to thediamine 112. Subsequently, the diamine can be reacted with nitrosubstituted benzoic acid 115 to prepare the benzimidazole 117. Thereduced molecule 118 can be converted to the desired guanidine andcarbamide substituted benzimidazole. The resulting molecules were orcould be purified using a combination of flash chromatography and/orrecrystallization. The resulting compounds were or could becharacterized by NMR spectroscopy, IR spectroscopy, melting point, andmass spectrometry.

The compounds of formula 6 wherein Ar is 1-napthylenyl; 2-napthylenyl;phenanthrenyl; anthracenyl,

wherein n is 0, 1, 2, or 3; or other analogs disclosed herein can begenerated in a similar fashion as illustrated in Scheme 2, with theselection of an appropriate analog of compound 110 in the reactionscheme.

Example 4 Synthesis of Cycloaliphatic-Substituted BenzimidazoleCompounds of Formula 7

The preparation of the cycloaliphatic-substituted benzimidazolecompounds may be accomplished using the synthetic route illustrated inScheme 3. Under microwave irradiation, the alkyl substituted amine 119may be coupled to 1-fluoro-2-nitrobenzene 109 to give the nitro diarylamine 120. The nitro group of the diaryl amine may be reduced using zincand ammonium chloride to produce the diamine 121. Reacting the diamineand the benzoyl chloride 113 together under reflux conditions couldgenerate compounds of formula 7. For general information, see: Goker, H.et al., Bioorganic. Medicinal Chemistry 2002, 10, 2589-2596. Theresulting molecules may be purified using a combination of flashchromatography and/or recrystallization.

Example 5 Synthesis of Cycloaliphatic-Substituted BenzimidazoleCompounds of Formula 8

Compounds of formula

can be prepared according to Scheme 3, using the benzoyl chloride

for preparing the compounds.

Example 6 Synthesis of Cycloaliphatic-Substituted BenzimidazoleCompounds of Formula 9

The preparation of aromatic-substituted benzimidazole compounds offormula 9 was accomplished using the synthetic route outlined in Scheme4. Under microwave irradiation, a 4-substituted aniline derivative 119was coupled to 1-fluoro-2-nitrobenzene 109 to give a nitro diaryl amine120 as previously described. The diaryl amine 120 can be reduced to thediamine 121. Subsequently, the diamine can be reacted with nitrosubstituted benzoic acid 115 to prepare the benzimidazole 124. Thereduced product 125 can be converted to the desired guanidine andcarbamide substituted benzimidazole. The resulting molecules were orcould be purified using a combination of flash chromatography and/orrecrystallization. The resulting compounds were or could becharacterized by NMR spectroscopy, IR spectroscopy, melting point, andmass spectrometry.

Example 7 Synthesis of Sulfonamide-Substituted Imidazopyridine Compoundsof Formula 10

The preparation of sulfonamide-substituted imidazopyridine analogs wasaccomplished using the synthetic route outlined in Scheme 5. Undermicrowave irradiation, a 4-substituted aniline derivative 110 wascoupled to 1-fluoro-2-nitrobenzene 126 to give a nitro diaryl amine 127.Using a domestic microwave, the reaction produced yields greater than99.5% when the aniline substituent was an electron donating group. (See:Xu, Z.; Lu, Y.; Guo, Z-R. Synlett., 2003, 564-566.) However, optimizingthe reaction conditions was difficult using a standard householdmicrowave and relied heavily on the placement of the vessel in themicrowave cavity to ensure reproducibility.

When the reaction was conducted in the CEM Discovery System, a singlemode industrial microwave able to maintain the temperature and pressureof the reaction mixture, the reaction time was decreased from 20 minutesto 5 minutes in some cases. The CEM reaction gave reproducible resultsand the crude reaction mixture showed no evidence of side products. Thenitro group of the diaryl amine was reduced using zinc and ammoniumchloride. After about 24 hours, approximately 90-100% of the nitrocompound 127 was reduced to the diamine 128. Ring formation was affordedfrom a condensation reaction of the diamine and the benzoyl chloride 113in two steps to give the target molecules 10. For general information,see: Goker, H.; Kus, C.; Boykin, D.; Yildiz, S.; Altanlar, N. Synthesisof Some New 2-Substituted-phenyl-1H-benzimidazole-5-carbonitriles andTheir Potent Activity Against. Candida Species. Bioorganic. MedicinalChemistry 2002, 10, 2589-2596. The analogs corresponding to formula 16,wherein X^(D) is

and wherein Ar is 1-napthylenyl; 2-napthylenyl; phenanthrenyl;anthracenyl;

wherein n is 0, 1, 2, or 3; or other analogs disclosed herein can begenerated in a similar fashion as illustrated in Scheme 1, with theselection of an appropriate analog of compound 110 in the reactionscheme. The resulting compounds were or could be characterized by NMRspectroscopy, IR spectroscopy, melting point, and mass spectrometry.

Example 8 Synthesis of Sulfonamide-Substituted Imidazopyridine Compoundsof Formulas 11, 12, and 13

Scheme 5 can be applied towards the synthesis of compounds of formulas11, 12, and 13 wherein X^(D) is

using the appropriate halogen substituted nitro pyridine

Example 9 Synthesis of Hydantoin-Substituted Imidazopyridine Compoundsof Formulas 10, 11, 12 and 13

The following compounds of formulas 10, 11, 12, and 13:

can be prepared according to Scheme 5, using the benzoylchloride

for preparing the compounds, and the appropriate halogen-substitutednitro pyridine as described above.

Example 10 Synthesis of Guanidine and Carbamide-SubstitutedImidazopyridine Compounds of Formula 10

The preparation of aromatic-substituted benzimidazole analogs wasaccomplished using the synthetic route outlined in Scheme 6. Undermicrowave irradiation, a 4-substituted aniline derivative 110 wascoupled to 1-fluoro-2-nitrobenzene 126 to give a nitro diaryl amine 127as previously described. The diaryl amine 127 can be reduced to thediamine 128. Subsequently, the diamine can be reacted with nitrosubstituted benzoic acid 115 to prepare the benzimidazole 117. Thereduced molecule 118 can be converted to the desired guanidine andcarbamide substituted benzimidazole. The resulting molecules 10 may bepurified using a combination of flash chromatography and/orrecrystallization.

Derivatives compounds of formula 16, wherein X^(D) is

wherein Ar is 1-napthylenyl; 2-napthylenyl; phenanthrenyl; anthracenyl;

wherein n is 0, 1, 2, or 3, or other analogs disclosed herein can begenerated in a similar fashion as illustrated in Scheme 1, with theselection of an appropriate analog of compound 110 in the reactionscheme.

Example 11 Synthesis of Sulfonamide-Substituted Imidazopyrazines andSulfonamide-Substituted Purines of Formulas 14, 15, 20 and 21

Scheme 5 can be applied towards the synthesis of the following compoundsof formulas 14 and 20:

by using

instead of 126. Scheme 5 can also be applied towards the synthesis ofthe following compounds of formulas 15 and 21:

by using

instead of 126.

Example 12 Synthesis of Hydantoin-Substituted Imidazopyrazines andHydantoin-Substituted Purines of Formulas 14, 15, 20 and 21

The following compounds of formulas 14, 15, 20, and 21:

and

can be prepared according to Scheme 5, using the benzoyl chloride

for preparing the compounds.

Example 13 Synthesis of Guanidine/Carbamide-Substituted Imidazopyrazinesand Guanidine/Carbamide-Substituted Purines of Formulas 14, 15, 20 and21

Scheme 6 can be applied towards the synthesis of the following compoundsof formulas 14 and 20:

with the use of

instead of 126. Scheme 6 can also be applied towards the synthesis ofthe following compounds of formulas 15 and 21:

Example 14 Synthesis of 7-Aromatic-Substituted Benzimidazole Compoundsof Formula 22

The preparation of 7-aromatic-substituted benzimidazole compounds havingthe formula 22 may be accomplished using the synthetic route outlined inScheme 7. Thus, compounds having the formula

in which X can be selected from H, C(CH₃)₃, phenyl, CF₃, OCF₃, OC(CH₃)₃,CH₃, OCH₃, or Cl, and other aryl groups disclosed herein can besynthesized as follows.

Compounds of formula 22 can be prepared by an initial carbon-carboncoupling of two aromatic rings, Scheme 7, according to the methoddisclosed in Ito, Y.; Kojima, Y.; Suginome, M.; Murakami, M. NewSynthesis of Quinoxaline Derivatives Based on Palladium CatalyzedOligomerization of 1,2-diisocyanoarenes. Heterocycles 1996, 42, 597-615.The heteroaromatic ring can then be reduced using lithium aluminumhydride. Completion of the synthesis can occur with a microwavecatalyzed condensation to form the benzimidazole ring, to provide thecompounds of formula 22.

The Grignard reagent of Scheme 7 and the thiadiazole protected diarylamine are readily available, and the reaction is known to proceed inyields greater than about 55%. Therefore, the Grignard approach is onedesired route for preparing compounds of formula 22, and there should befew side reaction products involving the thiadiazole ring.

Example 15 Alternative Syntheses of 7-Aromatic-Substituted BenzimidazoleCompounds of Formula 22

In an alternative reaction sequence, aromatic-substituted benzimidazolecompounds of formula 22 may be prepared through the synthesis ofcompound 134 according to Scheme 7. Compound 134 prepared in this mannerthen may be used in the synthetic route according to Scheme 8. Accordingto this method, compound 134 may be prepared from 132 utilizing a Suzukicross-coupling aided by an aryl boronic acid 135 and a palladiumphosphine catalyst (such as Pd(PPh₃)₄, as illustrated Scheme 8).

Example 16 Synthesis of 7-Aromatic-Substituted Benzimidazole Compoundsof Formula 23

Compounds of the formula

can be prepared according to Scheme 7, using the benzoyl chloride

for preparing the compounds.

Example 17 Synthesis of 7-Aromatic-Substituted Benzimidazole Compoundsof Formula 27

The preparation of 7-aromatic-substituted benzimidazole compounds havingthe formula

may be accomplished from compound 135 using the synthetic route outlinedin Scheme 9. Compound 135 can be prepared by methods previouslydescribed. According to the method, compound 135 can be condensed withthe nitro benzoic acid 115 to form the benzimidazole 137. The reducedmolecule 138 can be converted to the desired guanidine and carbamidesubstituted benzimidazole. The resulting molecules may be purified usinga combination of flash chromatography and/or recrystallization.

Example 18 Alternative Syntheses of Aromatic-Substituted BenzimidazoleCompounds of Formulas 3 and 6

Alternative syntheses of preparing the aromatic-substitutedbenzimidazole compounds of formulas 3 and 6 can be carried out asfollows. Referring to Scheme 10, which specifically illustrates thealternative synthesis for compounds of formula 3, benzoyl chloride (140)may used to accomplish the cyclization to form the benzimidazole.However, the yields are less than those obtained for the methoddescribed in Scheme 2.

Alternatively, a benzoic acid may be used in place of the benzoylchloride for the cyclization reaction shown in Scheme 11. The reactionsillustrated in Scheme 11 are also applicable to compounds of formulas1-2 and 4-5, while utilizing the appropriate substitutions. Thealternative is also useful in the preparation of compounds of formulas10-20 when the appropriate diamine precursor is used. Anotheralternative reaction carries out the cyclization in the presence of asodium bisulfite adduct of the appropriately substituted benzaldehyde(141e). These reactions may be conducted using the one-step microwaveprocedure disclosed herein, or alternatively, under reflux conditions toproduce the desired final product. Additional alternative cyclizationreagents for reaction with the diaryl amine include the imidate (141b),amide (141c) or nitrile (141d), in which R^(F), R^(G), and R^(H) areselected independently from H, an alkyl having up to about 10 carbonatoms, or an aryl group having up to about 14 carbons.

Example 19 Spectral and Analytical of Molecules

¹H NMR spectral data for the molecules was on a Varian INOVA 400 MHzspectrometer. Chemical shifts are expressed relative totetramethylsilane (TMS) and deuterated acetone.

N-(2-nitrophenyl)-2-naphthalenamine was obtained in 43% yield as ayellow solid. m/z 265.1 (M+H)⁺. ¹H NMR (CDCl₃, 400 MHz) δ 6.79 (t,J=15.2 Hz, 1H); 7.31 (d, J=8.8 Hz, 1H); 7.37-7.41 (m, 2H); 7.47-7.51 (m,2H); 7.72 (sd, J=1.6 Hz, 1H); 7.78 (d, J=7.2 Hz, 1H); 7.84 (d, J=7.6 Hz,1H); 7.88 (d, J=8.4 Hz, 1H); 8.22 (dd, J=10, 1.6 Hz, 1H); 9.5 (br s,1H).

4-Methyl-2′-nitrodiphenylamine was obtained as an orange solid. IR(mineral oil) 1507.34, 1598.48, 2343.80, 2918.48, 3030.66, 3316.19 cm⁻¹.¹H NMR (CDCl₃, 400 MHz) δ 2.4 (s, 3H); 6.71 (t, J=6.8 Hz, 1H); 7.13-7.26(m, 5H); 7.32 (t, J=6.8 Hz, 1H); 8.18 (dd, J=8.4, 1.6 Hz, 1H); 9.46 (brs, 1H).

4-Phenyl-2′-nitrodiphenylamine was obtained as an orange solid. ¹H NMR(CDCl₃, 400 MHz) δ 6.78 (t, J=6.8 Hz, 1H); 7.31-7.43 (m, 6H); 7.45 (t,J=6.4 Hz, 2H); 7.60-7.66 (m, 5H); 8.22 (dd, J=8.8, 1.2 Hz, 1H); 9.54 (s,1H).

4-Phenoxy-2′-nitrodiphenylamine was obtained as an red solid. ¹H NMR(CDCl₃, 400 MHz) δ 6.74 (t, J=7.2 Hz, 1H); 7.04-7.16 (m=5); 7.23 (m,3H); 7.35 (m, 3H); 8.19 (dd, J=8.8, 1.2 Hz); 9.45 (br s, 1H).

4-[1-(2-Napthalenyl)-1H-benzimidazol-2-yl)]Benzenesulfonamide (208) wasobtained as a white solid. m/z 400.1 (M+H)⁺. ¹H NMR (CD₃COCD₃, 400 MHz)δ 6.85 (d, J=8 Hz, 1H); 7.17-7.23 (m, 2H); 7.32 (t, J=14.4 Hz, 1H); 7.43(t, J=16 Hz, 1H); 7.56 (t, J=15.2 Hz, 1H); 7.68-7.73 (m, 6H); 7.84 (d,J=7.2 Hz, 1H); 8.11 (d, J=8.4 Hz, 1H); 8.17 (q, J=9.6 Hz, 1H).

4-(1-Phenoxy-1H-benzimidazol-2-yl)Benzenesulfonamide (210) was obtainedas a white solid. ¹H NMR (DMSO, 400 MHz) δ 7.2 (d, J=6.8 Hz, 1H);7.29-7.45 (m, 11H); 7.69 (d, J=8.8 Hz, 2H); 7.78 (d, J=8.8 Hz, 2H); 7.82(m, 1H).

4-(1-Phenyl-1H-benzimidazol-2-yl)benzenesulfonamide (211) was obtainedas a white solid. ¹H NMR (DMSO, 400 MHz) δ

4-[1-(4-methylphenyl)-1H-benzo[d]imidazol-2-yl]benzenesulfonamide (206)was obtained as a white solid. ¹H NMR (DMSO, 400 MHz) δ 2.3 (s, 3H); 7.2(d, J=6.8 Hz, 1H); 7.29-7.45 (m, 6H); 7.69 (d, J=6.4, 2H); 7.79-7.85 (m,3H).

4-(1-(4-benzylphenyl)-1H-benzo[d]imidazol-2-yl)benzenesulfonamide (209)was obtained as an off-white solid. ¹H NMR (DMSO, 400 MHz) δ 4.23 (s,2H); 7.20-7.47 (m, 1H); 7.7 (d, J=8.4 Hz, 2H); 7.79 (d, J=8.4 Hz, 2H);7.82 (d, J=8.0 Hz); 8.01-8.05 (m, 1H).

4-Sulfamoylbenzoyl chloride was obtained as a white solid. IR (mineraloil) 1157.02, 1340.30, 1719.63, 2964.05, 3252.65, 3331.67 cm⁻¹. ¹H NMR(DMSO, 400 MHz) δ 7.54 (s, 1H); 7.92 (d, J=8.0 Hz, 2H); 8.10 (d, J=8.40Hz, 2H).

4-(2,5-dioxoimidazolidin-4-yl)benzoyl chloride was obtained as a tansolid. IR (mineral oil) ¹H NMR (DMSO, 400 MHz) δ 3.28 (s, 1H); 5.291 (s,1H); 7.45 (d, J=8.8 Hz, 2H); 7.96 (d, J=8.0 Hz 2H) 8.48 (s, 1H).

Example 20 Methods for Structural Analysis

Fuzzy Pharmacophore. A fuzzy pharmacophore was generated ofOSU/Celecoxib analogs using the Pymol and the Liquid software plug-ins.See: DeLano, W. L. The PyMOL Molecular Graphics System (2002) DeLanoScientific, San Carlos, Calif., USA (www.pymol.org); Tanrikulu, Y.;Proschak, E.; Schneider G. LIQUID: Fuzzy Pharmacophore Models Based onTrivariate Gaussian Distributions, 2006, in preparation. The analysis ofthe inventive molecules was carried out by structural alignment, whichwas accomplished using the flexible alignment tool of MOE with defaultsettings and the MMFF94. The molecules were docked in the crystalstructure of PDK-1 in complex with ATP (PDB code 1H1W) using the GOLDsoftware. See: a) Nissink, J.; Murray, C.; Hartshorn, M.; Verdonk, M.;Cole, J.; Taylor, R. A new test set for validating predictions ofprotein-ligand interaction. Proteins 2002, 49, 457-471; and b)GOLD-Protein-Ligand Dockingwww.ccdc.cam.ac.uk/products/life_sciences/gold/. The fuzzy pharmacophorewas then generated for the docked structures with the highest GOLDscore.

Overlays. The inventive molecules were further analyzed using overlays.Thus, the B3LYP hybrid functional with a double-zetavalence-polarization DFT basis set was used to perform DFT geometryoptimizations on a 32-processor Xeon cluster using the NWChemcomputational chemistry program for parallel computers. See: NWChem, AComputational Chemistry Package for Parallel Computers, Version 5.0(2006), Pacific Northwest National Laboratory, Richland, Wash.99352-0999, USA; www.emsl.pnl.gov/docs/nwchem/nwchem.html. Thebenzimidazole and OSU structures were superimposed using the ‘superpose’function in Tinker and seen to substantially coincide. Jay Ponder.Tinker Molecular Modeling Package, version 4.2.dasher.wustl.edu/tinker/.

Docking. The docking was accomplished using the crystal structure ofPDK-1 complexed with ATP (PDB code 1H1W) subjected to the deletion ofheteroatoms (phosphoserine, glycerol and sulfate ions), and the additionof polar hydrogens. Missing atoms were added to Gln73, Arg75, Arg238,Glu303, Lys304, Glu348, Lys357, and the missing residues Glu233, Ser234,Lys235 and Gln236 were added using DS Visualizer v1.6 and the ExtensibleComputational Chemistry Environment. See: Accelrys®.www.accelrys.com/?lid=tab _(—) accelrys and Extensible ComputationalChemistry Environment. ecce.pnl.gov/; Accelrys, Inc., 10188 TelesisCourt, Suite 100, San Diego, Calif. 92121. The Gasteiger partial atomiccharges and the gas-phase minimum energy structure were computed withMOE using the MM94x force field and default parameters. See: ChemicalComputing Group, Molecular Operating Environment (MOE);www.chemcomp.com/. MOE was used to designate the rotable bonds in theligand and predict its bound conformations in the binding cavity. Thedocked protein-ligand structures with the most favorable hydrogenbonding to Ser160/Ala162, Glu209, Asp223 were then placed in a cubicsolvent box and energy minimized in the same manner as the ATP-boundstructure.

Calculation of Binding Energies. Binding affinities were calculatedusing the MM94x force field implemented in MOE by taking the differencebetween the energy of the bound system and the isolated protein andligand using the optimized protein-ligand complexes described above. Inall cases, the binding energies indicate favorable ligand binding.

Calculation of Lipophilicity and Molar Volume. The lipophilicities andmolar volumes reported in Table 1 were calculated for the energyminimized structure contained in the database using the QuaSAR module inthe MOE software.

Example 21 Methods for Biological Assay

Compounds 206-208 of Table 1 were analyzed for their ability to inhibitcell proliferation in human prostate cancer cells, the results of whichare illustrated in FIG. 1. Compound 206 was slightly more effective atdiminishing proliferation in PC-3 cells than its pyrazole counterpartcelecoxib (201). Comparative test compounds 203-205 demonstrate aninhibition similar to that of the OSU compounds. See: Ripple M. O. etal., Journal of the National Cancer Institute 1997, 89, 40-48. Modestlevels of kinase inhibition was observed for IKKβ and CK2. However,there was a significance reduction in activity for CDK1/cyclinB, GSK3β,and p70S6K in the presence of the benzimidazole compounds as illustratedin Table 2.

TABLE 2 Kinase Inhibition of Various Benzimidazole Compounds % Activity                                  Kinase

(209)

(210) CDK1/cyclinB(h) 36 16 CK2(h) 22 99 GSK3β(h)  5  7 IKKβ(h) 25 72p70S6K(h) 12 18 PDK1(h) 30 Not tested % Activity                                Kinase        

(206)

(211) CDK1/cyclinB(h)  7 11 CK2(h) 92 99 GSK3β(h) 72 13 IKKβ(h) 86 71p70S6K(h) 33 17 PDK1(h) Not tested Not tested

Cell Culture and Drug Treatment. PC-3 human prostate cancer cells wereseeded in duplicate 96 well tissue culture plates at 500 cells/well in80-μL Dulbecco's minimal essential medium (DMEM) supplemented with 5%fetal bovine serum (FBS) and nonessential amino acids and 1% equimolarmixture of streptomycin-penicillin. The flasks were incubated in ahumidified 95% air/5% CO₂ atmosphere. The cells were grown for at least24 hours to ensure that they were in the early log phase of growth.Cells were then treated with 20-μL drug solutions (stock 10 mM drugsolution in DMSO was diluted in DMEM containing 5% FBS such that finalDMSO concentration is less than 1%) of appropriate final concentrationby serial dilution. Untreated control cells received 20-μL DMEMcontaining 5% FBS. Six wells of each plate received the same drugconcentration. Thus, each data point and error bars are an average andstandard deviation of readings from 12 wells treated with identical drugconcentration.

DNA Assay. After appropriate time of incubation, DNA assay wasperformed. For DNA assay, each culture plate was washed with 25% PBS andincubated in deionized double distilled water for at least one hour atroom temperature. Plates were frozen at −70° C. and thawed/equilibratedto room temperature. Hoechst 33258 DNA binding dye was then added toeach well in 200-μL of high salt TNE buffer (10 mM Tris, 1 mM EDTA, 2 MNaCl [pH 7.4]) at a final concentration of 6.7-μg/mL. After furtherincubation at room temperature for 2 hours under protection from light,culture plates were scanned on the CytoFluor 2350™ scanner using the360/460 nm filter excitation and emission set. Readings from all plateswere normalized to the fluorescence of control untreated cells and alldata were expressed as the percent control.

Kinase Assays. Kinase assays were conducted by Millipore'sKinaseProfiler Service to determine the amount of ATP phosphorylationthat occurs in the presence of a benzimidazole molecule. Kinases assayedincluded IKKβ, CK2, CDK1/cyclinB, GSK3β, and p70S6K. The desired kinasewas treated with the benzimidazole compound The reaction were initiatedby the addition of the MgATP mix. After incubation for 40 minutes atroom temperature, the reaction is stopped by the addition of 3%phosphoric acid solution. 10 μL of the reaction was then spotted onto aP30 filtermat and washed three times for 5 minutes in 75 mM phosphoricacid and once in methanol prior to drying and scintillation counting.The kinase activity was measured radiometrically to determine the amountof ATP phosphorylation produced. All assays were done in triplicate.

1. A compound having the formula:

wherein J is selected from

wherein Z is selected from CH₂, NH, O, or S;

wherein Q is selected from CH₂, NH, O, or S;

wherein n is 1, 2, or 3; or

wherein X in each occurrence is selected from hydrogen; a halide; alinear or branched alkyl having up to 10 carbon atoms, optionallysubstituted with at least one halide; or an alkoxide having a linear orbranched alkyl group having up to 10 carbon atoms, optionallysubstituted with at least one halide; wherein X^(D) is selected from

and Y is selected from O or NH.
 2. A compound according to claim 1,having the formula:

wherein X is selected from hydrogen; a halide; a linear or branchedalkyl having up to 10 carbon atoms, optionally substituted with at leastone halide; or an alkoxide having a linear or branched alkyl grouphaving up to 10 carbon atoms, optionally substituted with at least onehalide; and Y is selected from O or NH.
 3. A compound according to claim1 having the formula:

wherein J is selected from

wherein X is selected from CH₃, C(CH₃)₃, or OCH₃;

wherein Z is selected from CH₂, NH, O, or S;

wherein Q is selected from CH₂, NH, O, or S; or

wherein n is 1, 2, or 3; and Y is selected from O or NH.
 4. Apharmaceutical composition comprising a therapeutically-effective amountof at least one compound according to claim 1 or apharmaceutically-acceptable salt thereof, and apharmaceutically-acceptable carrier.